Genetic changes in soybean cultivars derived from Heihe 54

Abstract

Soybean (Glycine max) variety Heihe 54 has played a crucial role in the Heihe soybean breeding program in China, contributing to the development of over 85 cultivars. To elucidate the genetic changes that have occurred across multiple generations of selection during soybean breeding, we conducted comprehensive genotyping analysis using the 180K Axiom SoyaSNP array on 42 varieties from the Heihe breeding gram, as as eight parental lines. Cluster analysis revealed four distinct groups, reflecting various breeding phases that incorporated diverse genetic resources as parental lines within the pedigree. A detailed examination of the graphical genotype profile across the genome identified preferred chromosome segments for specific breeding phases. These conserved blocks, which have been consistently maintained in descendant varieties during the extensive breeding period, likely harbor genes related to critical agronomic traits. This is exemplified by the consistent transmission of two segments located on chromosomes 18 and 20, which harbor the stem growth habit-related gene Dt2 and the leaflet shape-related gene Ln, respectively. The widespread cultivation of Heihe 43, a soybean cultivar developed within this pedigree, is attributed to its broad genetic base and the pyramiding of elite alleles from its parental lines. The identification of favorable chromosome segments provides valuable insight for agronomic traitrelated gene mining and targeted breeding in the future. ©

Headnote

Keywords:

Pedigree

Genetic diversity

Linkage block

Transmission

Breeding

ABSTRACT

Soybean (Glycine max) variety Heihe 54 has played a crucial role in the Heihe soybean breeding program in China, contributing to the development of over 85 cultivars. To elucidate the genetic changes that have occurred across multiple generations of selection during soybean breeding, we conducted comprehensive genotyping analysis using the 180K Axiom SoyaSNP array on 42 varieties from the Heihe breeding gram, as as eight parental lines. Cluster analysis revealed four distinct groups, reflecting various breeding phases that incorporated diverse genetic resources as parental lines within the pedigree. A detailed examination of the graphical genotype profile across the genome identified preferred chromosome segments for specific breeding phases. These conserved blocks, which have been consistently maintained in descendant varieties during the extensive breeding period, likely harbor genes related to critical agronomic traits. This is exemplified by the consistent transmission of two segments located on chromosomes 18 and 20, which harbor the stem growth habit-related gene Dt2 and the leaflet shape-related gene Ln, respectively. The widespread cultivation of Heihe 43, a soybean cultivar developed within this pedigree, is attributed to its broad genetic base and the pyramiding of elite alleles from its parental lines. The identification of favorable chromosome segments provides valuable insight for agronomic traitrelated gene mining and targeted breeding in the future.

© 2025 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NCND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

1. Introduction

During the early stages of soybean (Glycine max) breeding, old landraces were commonly utilized for crossing. According to pedigree analysis, the 564 soybean cultivars released in China between 1923 and 1992 can be traced back to 308 ancestral varieties, 230 of Which are landraces [1]. Similarly, 99% of North American soybeans released in 1947-1988 can be traced back to just 80 landraces [2]. As modern breeding techniques have evolved, breeders have become increasingly cautious in incorporating new landrace sources into their breeding programs, primarily due to concerns over potential linkage drag of unfavorable alleles. The prevalent use of elite cultivars or improved germplasm as parents, with the aim of maintaining the commercial characters of new cultivars, is thought to result in narrow genetic diversity, especially in breeding programs with a long history [3,4].

Currently, more than 40% of Chinese soybean production occurs in Heilongjiang province. Within this province, Heihe city is particularly notable as the largest prefecture-level city for soybean production, contributing approximately one-seventh of the total soybean production in China. Heihe 54, a cornerstone variety in the development of numerous soybean cultivars, was bred through a cross between cultivar Fengshou 1 and landrace Suoyiling within the breeding program of the Heihe Institute of Heilongjiang Academy of Agricultural Sciences (renamed Heihe Branch, Heilongjiang Academy of Agricultural Sciences in 2007). Heihe 54, which was released in 1967, has a semi-determinate growth habit and superior agronomic characteristics, such as short internodes, high pod density, and a 100-seed weight of 20 g. Heihe 54 demonstrates high yield potential in fertile soils and has served as both a widely cultivated variety and a foundational parent in the Heihe soybean breeding program [5]. From 1967 to 2005, Heihe 54 contributed to over 85 cultivars as a direct parent or ancestor [6], most notably Heihe 43. Since 2015, Heihe 43 has been the most widely planted soybean cultivar in China, with a total cultivation area of over eight million hectares.

To broaden the genetic base of Chinese soybeans, breeders have introduced foreign soybeans as parental germplasm during the development of improved cultivars with enhanced agronomic traits, including high yield, lodging resistance, and seed quality. In 1923-2005, 287 and 129 Chinese soybean cultivars were derived from introduced soybean cultivars Tokachi Nagaha and Amsoy, respectively [6]. Both Tokachi Nagaha and Amsoy have played crucial roles in the lineage of the highly valued Chinese soybean cultivar Suinong 14, a prominent variety that has been extensively cultivated on over two million hectares of land in China [7]. Over the decades of work by the Heihe breeding program, soybean introductions such as Heihe 1, Tokachi Nagaha, Amsoy, Dunn, and Maple Arrow have served as parental lines, with Heihe 54 acting as the founder cultivar. Despite the extensive history of soybean breeding in Heihe and the profound influence of Heihe 54 as a core parent/grandparent in commercial soybean breeding in Northeast China, spanning at least four generations, no studies have been conducted to trace the inheritance of chromosomes within the Heihe soybean pedigree.

The objectives of this study were (1) to identify chromosomal changes by performing high-density Single Nucleotide Polymorphism (SNP) analysis of accessions in the pedigree of Heihe soybeans; and (2) to elucidate the genetic modifications and the fixation of chromosomal segments that occurred during the breeding process. Our findings shed light on the genetic architecture underlying soybean improvement in the Heihe pedigree. In addition, our findings pave the way for developing markers for precision breeding, enabling the efficient introgression of favorable alleles and the acceleration of trait improvement in soybean.

2. Materials and methods

2.1. Plant materials

The use of Heihe 54 over decades of soybean breeding in Heihe has provided an opportunity to study chromosome inheritance by analyzing the pedigree of derived cultivars. A total of 42 cultivars, along with eight parental lines, were included in the analysis (Fig. 1; Table S1). The seeds of each accession were obtained from the Chinese National Soybean Genebank at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. The phenotypic data were obtained from official records from the National Germplasm Evaluation Program of China and from variety registration data at the time of cultivar release (Table 51).

2.2. DNA preparation and genotyping

DNA was extracted from the leaves of five individuals per accession using a Genomic DNA Purification Kit (Thermo Scientific, Vilnius, LT, USA). All 50 accessions were genotyped using the 180K Axiom SoyaSNP array (Affymetrix, Santa Clara, CA, USA), which contains 170,233 high-quality SNPs developed by re-sequencing 47 diverse soybean accessions [8]. To ensure comprehensive detection of rare alleles (present in fewer than four accessions) across the 50 accessions, these accessions were initially analyzed along with 410 additional soybean samples (348 cultivated and 62 wild soybeans). After the first filtering step (missing rate > 0.1, heterozygosity > 0.1, minor allele frequency < 0.05), 74,185 SNPs were retained. Subsequent filtering (missing rate > 0.05, heterozygosity > 0.05) reduced the dataset to 37,651 SNPs for further analysis.

2.3. Data analysis

Redundant neighboring markers were pruned using PLINK V1.9 [9] using a linkage disequilibrium (LD)-based sliding window approach (window size = 1000 kb, step size = 1 SNP, pairwise r2 threshold = 0.99). Within each LD block, the algorithm automatically selected a single representative marker based on the following criteria: (1) lowest missing data rate, (2) highest minor allele frequency (MAF), and (3) the most centrally located marker within each bin. Graphical genotypes of these 50 soybean accessions were produced using 1868 bin markers distributed across the 20 chromosomes, which were visualized using GGT 2.0 software [10]. Fengshou 1 (released in 1958) was selected as the reference genotype for graphical genotyping analysis; since Fengshou 1 is the direct parent of Heihe 54, its genome provides the ancestral baseline haplotype for tracing genetic inheritance patterns in the pedigree.

2.4. Genetic diversity and cluster analysis

Genetic distances among the 50 accessions, along with the genetic diversity index (7), were calculated using Tassel 5.0 software [11] based on a dataset comprising 37,651 SNPs. Subsequently, a neighbor-joining (NJ) tree was constructed using Mega software, with the tree topology derived from the distance matrix [12].

2.5. Sequence analysis of Ln in the soybean accessions

To characterize allelic variation of the Ln (leaflet shape) gene (Glyma20g25000), two primer pairs (Table S2) were designed based on the Williams 82 reference genome (Glyma.Wm82.a2.v1). The coding sequences of Glyma20g25000 from all accessions in the Heihe 54 pedigree were amplified and sequenced; polymorphic SNPs are summarized in Table S3.

3. Results

3.1. Genetic clustering reflects decades of pedigree development during Heihe soybean breeding

We carried out population genetic analysis of 50 Heihe soybean accessions, which resolved four distinct clusters that precisely mirrored the historical breeding trajectory, from founder lines to modern cultivars. Group 1 comprised Heihe 54, its parental lines Fengshou 1 and Suoyiling, Heihe 51 (which shares the common parent Fengshou 1 with Heihe 54), four progenies derived from Heihe 54, and the early breeding line Heihe 103. Group II included the ancestral introduction Heihe 1 and ten cultivars derived from this line. Group III contained four soybean introductions, namely Dunn, Amsoy, Maple Arrow, and Tokachi Nagaha, along with the parental cultivar Hefeng 26 and nine cultivars containing significant contributions from these four soybean introductions. Group IV consisted of 16 cultivars, all third- to fourth-generation descendants from Heihe 54 (Fig. 2). The genetic diversity (π) was 0.310 among the 50 soybean accessions but was lower within each of the four subgroups. Group I exhibited the highest π value of 0.252, closely followed by Group IV (0.242), Group III (0.225), and Group II (0.211). Overall, our data underscore the selection for genetic improvement that has occurred during the course of soybean breeding.

3.2. Conserved chromosomal blocks trace the inheritance of elite alleles from the founder cultivar Heihe 54

To trace the inheritance of elite alleles from the founder cultivar Heihe 54 and characterize its genomic contributions to modern soybean varieties, we used high-density SNP analysis to identify conserved chromosomal blocks transmitted across lineages. High-density SNP analysis revealed distinct chromosomal haplotypes for each lineage (Fig. S1), with ancestral alleles from Fengshou 1 shown in gray and derived variants in black. Notably, several linkage blocks were transmitted from the ancestor Heihe 54 to a substantial proportion of soybean cultivars derived from this line within the pedigree. These conserved blocks were located on chromosome 5 (Chr. 5) (8.8-26.7 Mb), Chr. 6 (17.6-31.9 Mb), Chr. 12 (8.9-24.3 Mb), Chr. 15 (20.7-40.3 Mb), Chr. 17 (32.2-39.2 Mb), and Chr. 18 (19.5-49.0 Mb). The presence of conserved chromosomal blocks spanning six chromosomes demonstrates that Heihe 54 as made substantial genomic contributions to modern elite soybean cultivars, remaining a critical source of elite alleles through its role as a founder parent.

3.3. Founder effects and chromosomal legacy of foreign introductions in Heihe soybean breeding

The initial phase of the Heihe soybean breeding program leveraged exotic introductions to diversify the genetic pools. To quantify the generational impact of key progenitor cultivars, we conducted manual pedigree tracing by systematically reviewing historical breeding records and cultivar registration documents. This analysis revealed that Amsoy, Heihe 1, and Tokachi Nagaha served as progenitors for 18, 29, and 34 cultivars, respectively (Table 51). Other soybean introductions were also incorporated into the breeding process. Notably, Maple Arrow served as the parental line of Heihe 20 and Heihe 28, while Dunn played a pivotal role as the parental line of Heihe 23 and Heihe 26 and served as the grandparental line of Heihe 41, Heihe 43, and Heihe 45 (Fig. 1; Table S1).

Dunn, Maple Arrow, Amsoy, and Tokachi Nagaha exhibited distinct chromosome structures compared to the other cultivars across most chromosomes (Fig. S1). A range of 35 to 92 rare alleles was observed in these introductions. Notably, Maple Arrow (92 rare alleles) and Dunn (90 rare alleles) exhibited the highest numbers of rare alleles, closely followed by Tokachi Nagaha (53 rare alleles). By contrast, Heihe 1 showed the fewest rare alleles, with only 35 (Fig. 3). Among the introductions, Tokachi Nagaha contributed the highest number of cultivars in the pedigree. Three segments on Chr. 3 (8.2-17.2 Mb, 24.7-28.6 Mb, and 36.3-42.8 Mb) were transmitted from Tokachi Nagaha to 19 cultivars belonging to Groups III and IV over four generations. Moreover, on Chr. 7, two linkage blocks (3.4-19.0 Mb, 39.8-44.5 Mb) were inherited from Tokachi Nagaha by eight cultivars in Group II. Similarly, a substantial linkage block (12.3-31.4 Mb) on Chr. 17 was transmitted from Tokachi Nagaha to five cultivars in Group II, and a smaller segment (19.1-31.4 Mb) was transmitted to the four remaining cultivars in the same group (Fig. 4A).

We also explored the contribution of Heihe 1, a soybean variety introduced from Russia, in genetic transmission among soybean cultivars. Notably, the majority of Chr. 1, spanning 10.5 to 55.3 Mb, was transmitted from Heihe 1 to Heihe 4. Following a recombination event within the 45.8-45.9 Mb region, a linkage block (45.9-55.3 Mb) was transmitted to seven cultivars in Group II. A linkage block on Chr. 3 (7.0-29.6 Mb) was transmitted from Heihe 1 to Heihe 103, Heihe 16, and Heihe 21. Additionally, five cultivars, Heihe 30, Heihe 31, Heihe 42, Heihe 23, Heihe 21, and Heihe 43, shared a conserved segment (11.7-27.8 Mb) on Chr. 10, which originated from Heihe 1. Furthermore, a linkage block (7.5-16.3 Mb) on Chr. 18 inherited from Heihe 1 was shared among nine cultivars (Fig. 4B). Together, these genomic transmission patterns demonstrate that Heihe 1 has contributed to the genetic architecture of current soybean cultivars through conserved chromosomal segments and recombination events.

By contrast, Amsoy did not transfer any apparent linkage blocks to any of the cultivars within this pedigree, even in the case of Heihe 5, whose direct parent is Amsoy. The sole linkage block transferred from Dunn to the four cultivars descended from this line was located on Chr. 14 (28.7-42.9 Mb). Additionally, Heihe 20 and Heihe 28 inherited two linkage blocks on Chr. 19 (0.1-15.2 Mb, 21.1-37.0 Mb), as well as the terminal segment of Chr. 10 (45.1 to 50.7 Mb) from their immediate parent Maple Arrow (Fig. S1).

3.4. Chromosome structure variation increased during soybean breeding

To investigate how chromosome structure variation emerged and evolved during the breeding of Heihe soybean cultivars, we analyzed genomic transmission patterns across four cultivar groups derived from different parental lineages. Our analysis revealed significant structure variation in specific chromosome regions among cultivars from different groups. For example, on Chr. 3, a linkage block ranging from 17.1 to 34.6 Mb was transmitted from Heihe 54 to the majority of cultivars in Groups I and II. Conversely, a novel segment within this region was shared among most cultivars in Groups III and IV (Fig. 51).

We further identified novel linkage blocks that originated from genetic recombination or introgression events in Heihe 54 - derived cultivars and became fixed during subsequent breeding. On Chr. 5, a linkage block (34.9-36.0 Mb) is commonly present in the majority of cultivars belonging to Groups II, III, and IV. This region is also shared among Heihe 1, Maple Arrow, and Tokachi Nagaha. A conserved region (17.0-19.9 Mb) on Chr. 20 was discovered in all cultivars descended from Heihe 54. Another conserved region on Chr. 20 (34.3-35.9 Mb) is shared among numerous cultivars belonging to Groups II, III, and IV (Fig. S1). Collectively, these results demonstrate that the introduction of diverse parental genomes alongside Heihe 54 has driven the emergence and fixation of novel chromosome structures, illustrating how breeding practices have shaped the dynamic evolution of genomic architecture in soybean cultivars.

3.5. Asymmetric parental inheritance drives elite trait integration in Heihe 43

To dissect the genetic basis of elite trait integration in Heihe 43, we investigated asymmetric parental inheritance patterns by analyzing SNP transmission from its parents (Heihe 18 and Heihe 23) across all chromosomes. Among the 414 polymorphic SNPs inherited by Heihe 43 from its parents, 199 originated from Heihe 18 and 215 from Heihe 23. The allelic inheritance pattern for each chromosome of Heihe 43, when traced back to its parental cultivars, displayed a notable imbalance. Specifically, eight of the 20 chromosomes exhibited significant deviations from the anticipated 1:1 parental contribution (χ2 goodness-of-fit test, P < 0.01). All SNPs on Chr. 5 and Chr. 12, as well as over 80% of the SNPs on Chrs. 1, 9, and 14, were inherited from Heihe 23. Conversely, more than 80% of the SNPs on Chrs. 6, 17, and 19 were inherited from Heihe 18 (Fig. 5). This skewed inheritance pattern suggests selective fixation of elite alleles during breeding, potentially explaining the exceptional adaptability of Heihe 43.

4. Discussion

4.1. Balancing founder effects and genetic diversity during Heihe soybean breeding

Pedigree analysis identified 41 key ancestors of Chinese soybean cultivars [13], several of which (e.g., Amsoy, Tokachi Nagaha) are also foundational parents in North American soybean breeding [14]. These findings point to the likely incorporation of beneficial alleles from these ancestors into soybean breeding activities in different breeding programs. The extensive use of a limited number of ancestors in specific soybean breeding programs has resulted in a decrease in genetic diversity and a narrow genetic base [14]. Although Heihe 54 served as the foundational ancestor for 39 cultivars (Fig. 1), only a slight reduction in the genetic diversity of the subpopulations was observed. This may be attributed to the continual incorporation of exotic soybean varieties into the breeding program.

Cluster analysis provided insight into how elite soybeans were utilized across various breeding stages. Specifically, Group I, which solely comprises the ancestors of Heihe 54 and several of its derived genotypes, is characterized by a relatively simple hybrid combination during the breeding process. Conversely, Group III contains introductions, among which Maple Arrow, Dunn, Tokachi Nagaha, and Amsoy demonstrate notable genetic divergence from the other cultivars (Fig. 2). This finding is consistent with the high frequency of rare alleles identified in these introductions (Fig. 3). The genetic clustering aligned remarkably well with the pedigree information, with only minor exceptions. For instance, Heihe 8 and Heihe 7 were nearly identical, even though Heihe 8 is a fast neutron mutant derived from Heihe 4. Additionally, according to pedigree information, Heihe 25 was derived through single-plant variation selection from the cultivar Heihe 14. Surprisingly, Heihe 25 shared a high degree of similarity (97.8%) with Heihe 35 and was thus grouped alongside this cultivar rather than with its ancestral cultivar Heihe 14 (Fig. 2).

4.2. Genomic basis of Heihe 43 dominance: Pyramiding elite alleles from divergent germplasm

The soybean cultivar Heihe 43, developed from a cross between soybean cultivars Heihe 18 and Heihe 23, demonstrated a yield increase of 8.8%-10.5% compared to Heihe 18 in consistent regional tests in 2005 and 2006 [15]. Released in 2007, Heihe 43 achieved an annual planting area of 83,000 ha in its inaugural year and has surpassed 670,000 ha since 2012. Heihe 43 has been the leading variety in China in terms of annual acreage since 2015. Based on a thorough analysis by its breeders, Heihe 43 is renowned for its exceptional characteristics, including early maturity, high yield, and resistance to frogeye leaf spot. The widespread adoption of Heihe 43 is primarily attributed to its wide genetic base, incorporating a multitude of soybean introductions in its lineage, including Heihe 1 from Russia, Tokachi Nagaha from Japan, and Dunn from the United States [16]. From the perspective of its genetic composition, Heihe 43 has pyramided the superior alleles of both parents. For instance, genomic analysis revealed that Chr. 5 (inherited entirely from Heihe 23) and Chr. 14 (82.4% from Heihe 23) contain QTL associated with protein content (GqPC5), plant height (6-g14), and days to maturity (10-g2) [17-19]. The terminal regions of Chr. 16 (4.0-5.1 Mb and 36.5-37.1 Mb), inherited from Heihe 18, harbor QTL related to protein content (6-g3, 4-g5) and seed-setting rate (1-g21) (Table S4) [20-22]. These segments have undergone stable transmission for three generations, tracing back to Heihe 9. The relatively few rare alleles in Heihe 43 (Fig. 3) and its phenotypic performance (Table S1) suggest that the combination of these elite haplotypes may contribute to its improved characteristics. Future studies should further dissect the contributions of these chromosomal segments to the broad adaptability of Heihe 43.

4.3. Functional genomic regions underlying agronomic trait selection during Heihe soybean breeding

In traditional soybean breeding, breeders select favorable allele combinations associated with specific agronomic traits. Our analysis revealed several conserved genomic blocks (Chrs. 5, 6, 12, 15, 17, and 18) that were stably inherited from Heihe 54 across multiple generations (Fig. S1). These regions harbor validated genes and QTL related to key agronomic traits, including maturity (E71), seed protein content (GqPC6), seed coat cracking resistance (qSC20), and 100-seed weight (Glyma.05G019200) (Table S4) [18,23-25]. Phenotypic data confirmed that these traits (e.g., early maturity, high protein content) were consistently inherited by the progeny lines (Table S1), supporting the functional importance of these conserved genomic segments, although the precise genetic mechanisms underlying the beneficial traits conferred by certain regions remain to be fully elucidated.

We identified a segment (59.5-60.1 Mb) on Chr. 18 that has been conservatively transmitted for several generations. This segment encompasses the Dt2 gene (Glyma18g50910), which confers the semi-determinacy trait in the Dt1Dt1 background [26]. Among the 39 semi-determinate soybean cultivars, 37 share the same haplotype in this region, with only two exceptions: Heihe 54 and Heihe 11. Despite being semi-determinate, these two cultivars share the same haplotype as the indeterminate cultivar Heihe 51 (Fig. 6A). This suggests that other loci might be involved in regulating stem growth, as evidenced by the rare recessive allele of dt3 found on Chr. 10 in semi-determinate soybeans from the USDA Germplasm Collection [27].

Another conserved transmitted segment (34.3-35.9 Mb) on Chr. 20 harbors the Ln locus [28]. The Ln genotype is related to narrow leaflets and a higher number of seeds per pod; Chinese soybean cultivars possessing the Ln allele are predominantly found in the northeast region [28-30]. Over the past four decades, the Heihe soybean breeding program has focused on developing elite soybean cultivars with narrow leaflets. Sanger sequencing of the 50 accessions in the current study identified the Ln allele (carrying a C nucleotide) in 29 narrow-leaflet accessions, while all broadleaflet accessions carried a G nucleotide (Table S3). At least three narrow leaflet-related haplotypes were observed in this genetic region (Fig. 6B), suggesting that Ln resources originated from diverse germplasm. The narrow-leaflet soybean cultivar Tokachi Nagaha has been used as an important elite resource in numerous breeding programs [31,32]. The incorporation of Tokachi Nagaha and Amsoy increased the seed number per plant and seed protein content of cultivars in the pedigree of Suinong14 [33]. It appears that the linkage block encompassing the Ln locus from Tokachi Nagaha was transmitted to Heihe 31 and Heihe 42 (Fig. 6). Additionally, an SNP marker within another conservatively transmitted region on Chr. 20 (16.3-19.9 Mb) is significantly associated with seed oil and protein contents [22].

The extensive transmission of Tokachi Nagaha-derived segments on Chr. 3 across 19 cultivars (Fig. 4A) overlaps with QTL associated with 100-seed weight (qHSW-3-2) and protein content (GqPC3) [18,34]. Regions on Chr. 7 harbor two protein-related QTL [20], while a block on Chr. 17 contains a QTL related to pod number [35]. Similarly, Heihe 1-derived segments on Chrs. 1, 3, 10, and 18 were retained in multiple soybean cultivars (Fig. 4B). These regions contain QTL related to protein content, seed weight, and pod number (Table S4) [35-38]. The consistent retention of these regions reflects how selection has been carried out to achieve the breeding objectives of the Heihe breeding program, including improved yield, quality, and adaptation.

The soybean cultivar Maple Arrow exhibits remarkable chilling tolerance and robust resistance to Sclerotinia sclerotiorum (SWM) [39,40]. As a direct parent of Heihe 28, Maple Arrow transmitted a 3.4 Mb chromosome segment (17.3-20.7 Mb) on Chr. 8 to Heihe 28 (Fig. S1). Within this segment, Qsp-3, a locus related to SWM, was mapped in Maple Arrow [41], suggesting potential inheritance of SWM resistance-related genomic regions in Heihe 28. Furthermore, the conserved chromosome regions shared by Maple Arrow, Heihe 20, and Heihe 28 on Chr. 10 and Chr. 19 harbor multiple yield- and quality-related QTL, as reported previously (Table S4) [21,36,42].

Cool weather is a significant factor influencing soybean production. Soybean lines with tawny pubescence carrying the T allele on Chr. 6 exhibit enhanced cold tolerance during later stages of growth [43]. Among the soybean cultivars descended from the Heihe 54 pedigree, only three lines possess tawny pubescence (Table S1). Heihe 20 and Heihe 28 share an identical tawny haplotype at the T locus, which was inherited from Maple Arrow. These super-early maturing cultivars, with a maturity period of 85-90 d, are specifically adapted to the extremely cold conditions for soybean cultivation in Northeast China, where the >10 °C accumulated temperature is only 1700-1850 °C, demonstrating the cold adaptability of these cultivars in field production. It appears that the breeders involved in the Heihe breeding program favored gray pubescent soybeans over tawny ones, perhaps because low temperatures during the flowering and filling stages in Heihe are less problematic than those encountered during the emergence stage and earlier stages of seedling growth [44]. The specific reasons for selecting gray pubescent soybeans, along with the transmission of diverse chromosome segments during the breeding process within this program, await further investigation.

CRediT authorship contribution statement

Rongxia Guan: Writing - review & editing, Writing - original draft, Resources, Funding acquisition. Luyan Zhang: Writing - original draft, Software, Data curation. Huawei Gao: Investigation, Funding acquisition. Huilong Hong: Resources. Dezhi Han: Validation. Ruzhen Chang: Supervision. Lijuan Qiu: Writing - review & editing.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

This work was supported by a Biological Breeding-National Science and Technology Major Project (2022ZD040190301) and the Agricultural Science and Technology Innovation Program (CAAS-CSNCB-202301).

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ARTICLE INFO

Article history:

Received 14 February 2025

Revised 28 May 2025

Accepted 29 May 2025

Available online 16 June 2025

References

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Footnote

* Corresponding authors.

E-mail addresses: [email protected] (K. Guan), [email protected] (L. Qiu).

1 These authors contributed equally to this work.