The Genetic Makeup of a Global Barnyard Millet Germplasm Collection

Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this crop in either cultivated species [E. colona (L.) Link and E. crus-galli (L.) P. Beauv.]. Recently, a core collection of 89 barnyard millet accessions was developed at the genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). To enhance the use of this germplasm and genomic research in barnyard millet improvement, we report the genetic characterization of this core collection using whole-genome genotyping-by-sequencing. We identified several thousand single-nucleotide polymorphisms segregating in the core collection, and we use them to show patterns of population structure and phylogenetic relationships among the accessions. We determine that there are probably four population clusters within the E. colona accessions and three such clusters within E. crus-galli. These clusters match phylogenetic relationships but by and large do not correspond to classification into individual races or clusters based on morphology. Geospatial data available for a subset of samples indicates that the clusters probably originate from geographic divisions. In all, these data will be useful to breeders working to improve this crop for smallholder farmers. This work also serves as a case study of how modern genomics can rapidly characterize crops, including ones with little to no prior genetic data

Author Correction: A chickpea genetic variation map based on the sequencing of 3,366 genomes

In Extended Data Fig. 1 of this Article, the labels ‘Market class’ and ‘Biological status’ were inadvertently swapped. In the corresponding figure legend, “Track 1: Biological status; Track 2: Market class;” should have been “Track 1: Market class; Track 2: Biological status;”. The original Article has been corrected online

Harnessing genetic diversity of Wild Arachis species for genetic enhancement of cultivated peanut

Peanut (Arachis hypogaea L.) is an important self-pollinating tetraploid (AABB, 2n = 4x = 40) legume grown for the high-quality edible oil and easily digestible protein in its seeds. Enormous genetic variability is present in the genus Arachis containing 79 wild species and cultivated peanut. Wild species offer significant variability, particularly for biotic and abiotic stresses, and can be used to develop cultivars with enhanced levels of resistance to key stresses. However, utilization of these species requires use of ploidy manipulations, bridge crosses, and embryo or ovule rescue. For efficient use of diploid wild species from section Arachis, several synthetics (amphidiploids and autotetraploids) have been developed using A- and B-genome accessions with high levels of resistance to multiple stresses. These synthetics are used in crossing programs with cultigens to develop prebreeding populations and introgression lines (ILs) with high frequency of useful genes and alleles into good agronomic backgrounds. Evaluation of two such populations derived from ICGV 91114 × ISATGR 121250 (a synthetic derived from A. duranensis Krapov. & W.C. Greg. × A. ipaensis Krapov. & W.C. Greg.) and ICGV 87846 × ISATGR 265-5 (A. kempf-mercadoi W.C. Greg. & C.E. Simpson × A. hoehnei Krapov. & W.C. Greg.) resulted in the identification of ILs with high levels of late leaf spot (LLS) and rust resistance and significant genetic variability for morphoagronomic traits. Genotyping of these ILs with markers linked to rust and LLS resistance provided evidence that introgression of possible novel alleles and resistance sources from different wild species other than the commonly used A. cardenasii Krapov. & W.C. Greg. will be beneficial for peanut improvement

Reakcja pyleńca pospolitego (Berteroa incana L.) na promieniowanie UV-B

This greenhouse experiment evaluated the response of hoary alyssum plants, up to the rosette phase, to different levels of UV-B radiation. The experiment was carried out in the chambers, equipped with UV-B lamps, emitting biologically effective UV-B radiation of 0 (control), 4, 6 or 8 kJ. As a result, specific traits of the plants such as: leaf number, lamina length, leaf area, specific leaf weight, relative chlorophyll content and shoot biomass were unaffected by any of the UV-B treatments. Significant reductions in the share of large leaves, leaf stalk length and root biomass were noted for plants growing under 8 kJ UV-BBE.Celem pracy było zbadanie reakcji pyleńca pospolitego (Berteroa incana L.), do fazy rozety liściowej, na promieniowanie UV-B. Doświadczenie przeprowadzono w warunkach szklarniowych, w komorach wyposażonych w lampy emitujące biologicznie czynne promieniowanie UV-B w stężeniu: 0 (kontrola), 4, 6 i 8 kJ. W wyniku przeprowadzonych badań stwierdzono, że zastosowane promieniowanie nie wpływało na takie cechy roślin, jak: liczba liści, długość blaszki liściowej, powierzchnia liści, specyficzna masa liści (SLW) oraz względna zawartość chlorofilu (w jednostkach SPAD) i masa części nadziemnych. Natomiast zaobserwowano istotną redukcję w udziale dużych liści, w długości ogonków liściowych i biomasie korzeni u roślin eksponowanych na najwyższe, 8 kJ UV-BBE, promieniowanie UV-B

Thermal weed control

This chapter reviews the major findings on thermal weed control for field crop

Identification of introgression lines with superior pod yield and improved rust resistance in peanut (Arachis hypogaea L.)

A major QTL explaining up to 82.62% of phenotypic variation for rust resistance was introgressed into three popular peanut varieties (TAG 24, ICGV 91114, JL 24) using marker-assisted backcrossing (MABC) approach. The donor parent, GPBD 4 derived its resistance from one of its interspecific parent, ICGV 86855 (CS 16), which in turn received from a diploid wild species, Arachis cardenasii. Four linked markers (IPAHM103, GM2079, GM1536, and GM2301) present in the QTL region were employed for foreground selection. Preliminary yield evaluation of 51 introgression lines (ILs) (17 of TAG 24, 13 of ICGV 91114 and 21 of JL 24) along with parents and checks showed significant differences among the lines for yield parameters and rust resistance. The pod yield of ILs was up to 56-96% higher than recurrent parents. The superior pod yield in ILs is in part attributed to pod yield protection offered by resistance. The ILs were resistant to rust with a disease score of 2.0 or 2.5 at 90 DAS (on 1-9 scale) similar to donor parent, while the recurrent parents had higher score (5.0 in TAG 24, 6.5 in ICGV 91114, 7.0 in JL 24). Disease progress from 75 to 90 days was slower in ILs. The differences were not significant for days to flowering between ILs and their respective recurrent parents. Combining disease resistance and early maturity in peanut varieties is the most significant outcome. Further evaluations and promotion of promising ILs to multi location evaluation will facilitate nominations to varietal release trials

Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut