Genetic Dissection And Genomic Selection Of Seed Weight,Pod Length And Pod Width In Soybean

Wealthy in protein and oil,soybean is one of the most important grain,oil and cash crops in the world.As the original country of soybean,domestic soybean production is far from meeting the domestic requirements of soybean consumption,and soybean imports rank first in the world.Therefore,soybean yield has always been one of the breeding objectives of Chinese breeders.The yield per plant of soybean is mainly composed of hundred-seed weight（100-SW）,effective pod number per plant,and seed number per pod.Physiologically,soybean pods provide physical space and nutrients for seed development and it’s size is highly positively correlated with seed size.Hence,it is necessary to mine QTLs for 100-SW and pod size（Pod length:PL;Pod width:PW）of soybean and study their genetic regulation mechanism and genetic relationship between them,which is of great significance for accelerating the breeding selection process of high-yield soybean and improving soybean per unit yield.In this study,364 recombinant inbred lines obtained from the cross of cultivated soybean Zhongdou 41×wild soybean ZYD02878 were used as research materials.The phenotypic identification and descriptive statistical analysis of 100-SW,PL,and PW in three environments were carried out.Based on the constructed genetic linkage map,several genetic analysis methods（ICIM,RTM-GWAS,3Vmr MLM and conditional GWAS）were used to identify QTL associated with100-SW,PL and PW,and candidate genes were further prioritized by analyzing SNP variation,fixation index,gene expression and functional annotation in the candidate interval.Based on the QTL mapping results,a multi-trait selection index-assisted genomic selection model was constructed.The main results are as follows:1.Base on the three environments（2019-JZ,2019-SY,2020-JZ）and multi-environment BLUE values,the 100-SW,PL and PW of cultivated soybean female parent were 23.81-26.02 g,47.57-60.50 mm and 10.07-10.52 mm respectively,which were significantly higher than those of wild soybean male parent（2.11-3.04 g,22.50-24.25 mm,5.07-5.99 mm）.In RIL population,100-SW,PL and PW approximately obey normal distribution.There was a significant positive correlation between 100-SW,PL and PW in different environments,and the correlation between 100-SW and PW was the highest（0.64-0.74）.In addition,significant correlations were also observed for the three traits among the three environments,respectively,indicating high data consistency among environments.The environment had the greatest effect on 100-SW and the least on PW,which is consistent with its generalized heritability calculations（PW:0.76;PL:0.75;100-SW:0.72）.2.A total of 219 QTL were identified by three different methods,ICIM,RTM-GWAS and 3Vmr MLM,of which 24 QTL intervals were co-localized by two to three methods.Based on q SW20-3,q PL3-4 and q PW4-3,conditional GWAS analysis identified 19 QTL loci with possible pleiotropy,of which Chr13:27,428,227..27,549,836 were associated with 100-SW,PL and PW.Through SNP variation analysis,fixation index calculation,gene expression analysis and functional annotation analysis of 284 genes in the interval of repeated identified by different methods and conditional GWAS detection,11 candidate genes,including ST1,were identified as potentially relevant to domestication,laying a solid foundation for further analysis of the molecular regulatory mechanisms of 100-SW and pod size.3.Among the 11 candidate genes,seven were related to 100-SW,three to PW,and one to 100-SW and PL,respectively.Seven 100-SW candidate genes regulated soybean seed size through pectin biosynthesis,ubiquitin-mediated protein degradation,cell proliferation,seed coat permeability,cell wall synthesis,embryo development and auxin.Auxin not only promotes normal embryo development but also controls pod size by regulating cell dimensions.The PW candidate gene Glyma.11G180900 encodes nitrilase4 which converts indole-3-acetonitrile into auxin.In addition to auxin,brassinosteroid can regulate soybean pod size by causing cell hypertrophy.Glyma.08G016400’s homologous gene At XPB1 regulates soybean pod size by regulating FPS2 to control the level of brassinosteroid.Another PW candidate,Glyma.11G181100,encodes photosystem I subunit O which participated in the balance of excitation pressure between the two photosystems.Similarly,Glyma.01G030500,a candidate gene associated with 100-SW and PL,affects seed and pod size via the photosynthetic pathway,and it encodes carbonic anhydrase 2,which is an upstream regulator of CO₂-controlled stomatal movement in guard cells.4.Based on the molecular markers contained in the QTL mapping interval,a GS model of 100-SW,PL and PW was constructed.Based on GUM,the prediction accuracy of 100-SW,PL and PW was 0.64,0.63 and 0.71,respectively.After adding TTAM as a random effect,it increased by 3.13%,4.76%and 2.82%respectively,while TTAM as a fixed effect greatly reduced the prediction accuracy（56.25%,82.54%and 76.06%）.In the six marker sets,the GS model constructed by the single trait QTL-associated markers had the highest prediction accuracy,reaching 0.82,0.76 and 0.86 respectively,while the selection index-assisted genome selection effect was not significant,only for GM and GUM marker sets.